Genotype imputation of case-control cohorts was performed using the pre-phasing/imputation stepwise approach implemented in EAGLE 2 / MINIMAC357,58 with 132 genomic windows of variable size and default parameters. The imputation reference consisted of 54,330 phased haplotypes with 36,678,882 variants from the publicly available HRC reference, release 1.1.59 Chromosome X imputation was conducted using individuals passing quality control for the autosomal analysis. Chromosome X imputation and association analysis was performed separately for males and females.
